A family of northern white-cheeked gibbons (Nomascus leucogenys) “lounging” in the tropical forest of Yexianggu, China. Males from this species are black, while females are blond. Babies are all born blond and turn black around half year of age; female start changing back to blond at the age of sexual maturity (about 6 years). Credit: Heather Angel/Natural Visions

With the completion of the sequencing and analysis of the gibbon genome, scientists now know more about why this small ape has a rapid rate of chromosomal rearrangements, providing information that broadens understanding of chromosomal biology.

Chromosomes, essentially the packaging that encases the genetic information stored in the DNA sequence, are fundamental to cellular function and the transmission of genetic information from one generation to the next. Chromosome structure and function is also intimately related to human genetic diseases, especially cancer.

The sequence and analysis of the gibbon genome (all the chromosomes) was published today in the journal Nature and led by scientists at Oregon Health & Science University, the Baylor College of Medicine Human Genome Sequencing Center and the Washington University School of Medicine's Genome Institute.

"Everything we learn about the genome sequence of this particular primate and others analyzed in the recent past helps us to understand human biology in a more detailed and complete way," said Dr. Jeffrey Rogers, associate professor in the Human Genome Sequencing Center at Baylor and a lead author on the report. "The gibbon sequence represents a branch of the primate evolutionary tree that spans the gap between the Old World Monkeys and great apes and has not yet been studied in this way. The new genome sequence provides important insight into their unique and rapid chromosomal rearrangements."

For years, experts have known that gibbon chromosomes evolve quickly and have many breaks and rearrangements, but up until now there has been no explanation why, Rogers said. The genome sequence helps to explain the genetic mechanism unique to gibbons that results in these large scale rearrangements.

The sequencing was led by Dr. Kim Worley, professor in the Human Genome Sequencing Center, and Rogers, both of Baylor and Drs. Wesley Warren and Richard Wilson of Washington University.

The analysis was led by Dr. Lucia Carbone, an assistant professor of behavioral neuroscience in the OHSU School of Medicine and an assistant scientist in the Division of Neuroscience at OHSU's Oregon National Primate Research Center. Carbone is an expert in the study of gibbons and the lead and corresponding author on the report.

A female northern white-cheeked gibbon (Nomascus leucogenys). Her baby is clinging to her as she is leaping from a branch to another (Yexianggu, China). Gibbons use brachiation to move through tropical rainforests and their transfers (as the one captured here) are often acrobatic. Credit: Heather Angel / Natural Visions
"We do this work to learn as much as we can about gibbons, which are some of the rarest species on the planet," said Carbone. "But we also do this work to better understand our own evolution and get some clues on the origin of human diseases."

Chromosomal biology

Chromosomes play an essential role in the packaging of DNA, Worley said. "There are 3 billion base pairs of DNA in every cell and it is packaged into 23 pairs of chromosomes," said Worley, also a lead author on the report.

When there are rearrangements in chromosomes, the genes and gene regulation are often disrupted or broken, said Worley.

"Cancer is clearly the biggest medical example of the impact of chromosome rearrangements. The gibbon sequence gives us more insight into this process," said Worley. "There are also a number of other genetic diseases that result from these events."

Rearrangements

The number of chromosomal rearrangements in the gibbons is remarkable, Rogers said. "It is like the genome just exploded and then was put back together," he said. "Up until recently, it has been impossible to determine how one human chromosome could be aligned to any gibbon chromosome because there are so many rearrangements."

Repeat element

The sequencing project revealed a novel and unique genetic repeat element (segments of DNA that occur in multiple copies throughout the genome) that is inserted into genes associated with the maintenance of chromatin structure.

Repeat elements have the capability to disrupt a gene and change their biological function, Worley said. In the gibbons, the team identified the LAVA element - a novel repeat element that emerged exclusively in gibbons and preferentially hits genes involved in chromosome segregation (an essential step in cell division, where chromosomes pair off with their similar homologous chromosome.)

"This explains why the gibbons have undergone so much change," said Rogers. "Similar disruptions cause disease, which is why everything we learn from this helps us better understand human biology and chromosomal structures."

Related Stories

When talking about genetic abnormalities at the DNA level that occur when chromosomes swap, delete or add parts, there is an evolving communication gap both in the science and medical worlds, leading to inconsistencies in ...

A team of scientists from around the world led by Baylor College of Medicine and Washington University in St. Louis has completed the genome sequence of the common marmoset – the first sequence of a New World Monkey – ...

The Glanville fritillary has long been an internationally known model species for ecology and evolutionary biology, whose population biology has been studied on the Åland Islands for more than twenty years. Now the species ...

Biologists reported today in Nature that they have identified two pathways through which chromosomes are rearranged in mammalian cells. These types of changes are associated with some cancers and inherited disorders in people.

Several Kansas State University researchers were essential in helping scientists assemble a draft of a genetic blueprint of bread wheat, also known as common wheat. The food plant is grown on more than 531 million acres around ...

An international scientific collaboration led by Baylor College of Medicine has revealed clues about genetic alterations that may contribute to a rare form of kidney cancer, providing new insights not only into this rare ...

Recommended for you

Past studies have found that a variety of complex networks, from biological systems to social media networks, can exhibit universal topological characteristics. These universal characteristics, however, do not always translate ...

Metasurfaces are two-dimensional (2-D) metamaterials that can control scattering waves of a light beam. Their applications include thin-sheet polarizers, beam splitters, beam steerers and lenses. These structures can control ...

The Transiting Exoplanet Survey Satellite (TESS) was launched on April 18 of last year with the primary objective of discovering transiting planets smaller than Neptune around stars bright enough for spectroscopic investigations ...

A pair of researchers at Purdue University has found a way to use a diatomic Ni-Ni catalyst to synthesize cyclopentenes. In their paper published in the journal Science, You-Yun Zhou and Christopher Uyeda describe their method ...

Photocatalysts – materials that trigger chemical reactions when hit by light – are important in a number of natural and industrial processes, from producing hydrogen for fuel to enabling photosynthesis.

Neutron stars are among the densest-known objects in the universe, withstanding pressures so great that one teaspoon of a star's material would equal about 15 times the weight of the moon. Yet as it turns out, protons—the ...

24 comments

If you are still an evolutionary theorist, human ethologist, or evolutionary biologist who believes that evolutionary events link mutations and/or natural selection to the evolution of biodiversity, don't tell anyone until all this information about RNA-mediated amino acid substitutions and chromosomal rearrangements blows over.

Alternately, set your sights on becoming a serious scientist, since this is not going to blow over.

If you ever commented positively about anything PZ Myers ever said, try to retract what you said before anyone realizes you said it -- unless you are an anonymous fool. Then, you need only hope that your name is not Andrew Jones, since only he was ignorant enough to criticize my most recent published work and cite PZ.

Odors induce the de novo Creation of odor receptor genes that link nutrient uptake to RNA-mediated events and pheromone-controlled cell type differentiation that limits species specific reproduction in the context of chromosomal rearrangements.

I hope that PZ Myers enjoys the publicity you have given him now that the chromosomal rearrangements have been linked from ecological variation to RNA-mediated events and ecological adaptations manifested in the morphological and behavioral phenotypes of species from microbes to man.

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of .."

My conclusion: "... the largest contributor to the development of our personal preferences may be the unconscious epigenetic effects of food odors and pheromones on hormones that organize and activate behavior. If so, the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific 'fit'." http://www.ncbi.n...24693353

It would be great if someone who is not an anonymous fool or idiot minion of PZ Myers would review my published work and comment now that the information about nutrient-dependent pheromone-controlled RNA-mediated chromosomal rearrangements extends from microbes to man via birds and other primates without the pseudoscientific nonsense of mutations and natural selection.

I'll take that as a "no" to my question. You make the claim that pheromones induce chromosomal rearrangements, but you can't support it with a citation. The same goes for your claim of creation of olfactory receptor genes. You talk about mediated changes in gene EXPRESSION (straight from your paper's abstract), but there's no mention of gene creation, so I'd like to see a citation for that.

I did a ctrl+F search for every instance of "gene" in your paper, but no instance regarded gene creation.

I wrote:"It would be great if someone who is not an anonymous fool or idiot minion of PZ Myers would review my published work and comment now that the information about nutrient-dependent pheromone-controlled RNA-mediated chromosomal rearrangements extends from microbes to man via birds and other primates without the pseudoscientific nonsense of mutations and natural selection."

The anonymous fool again tries to engage me in pointless discussion and tells others that I claimed pheromones induce chromosomal rearrangements.

Note, however, he never addressed any of the citations I included in my published review. What good does it do to cite works when the citations are ignored by PZ Myers idiot minions and other evolutionary theorists who know nothing about cell type differentiation?

Again, I ask for evidence that pheromones actually control (induce) those.

Note, however, he never addressed any of the citations I included in my published review.

I have pointed out how your citations don't support your claims on many occasions. Your misinterpretation of Nei's biophysical constraints, Darwin's terms, claiming the peppered moth coloration was due to what they ate rather than predatory selection, your claim that mutations theory does not address pleiotropy or epistasis, your claim that proteasomes mediate protein folding, your misinterpretation of Chelo et al., your comment on the Educate Truth blog where you thought citrate created an ORG in Lenski's E. coli, etc.

"Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans" exemplifies the nutrient-dependent link from the epigenetic landscape to the physical landscape of DNA in the organized genome of C. elegans. http://www.cell.c...)00806-X

C. elegans is the model organism often used to link the conserved molecular mechanisms of RNA-mediated cell type differentiation to morphological and behavioral phenotypes in humans that pseudoscientists think somehow 'evolved.'

Thanks. Someone must have told you that your citations were invalidated by works that detailed what are obviously nutrient-dependent pheromone-controlled RNA-mediated events -- exemplified in this article on the gibbons.

Recent reports:"It has 20 copies of the same chromosome when it's growing happily under favorable conditions, and 10 when nutrients are exhausted and it reaches a stationary phase." http://phys.org/n...ier.html

Here is an opportunity for anonymous fools PZ Myers' idiot minions to tell us how mutations and natural selection led to the chromosomal rearrangements reported across species in the context of experimental evidence showing the rearrangements are RNA-mediated events.

P Z Myers rose to become an internationally known University Professor...

"I followed up on a link to the "rule of 48" and picture of Little PZ Myers, who is the biology teacher most responsible for teaching the idiot minions and anonymous fools here to value theory rather than biological facts."

http://www.scribd...nalpaper "...plants generally have evolved...through a currently unknown mechanism (although genes involved and their effects have been identified (Pyke, 1999))"

Q: How did plants evolve? A: The genes and mechanism have not been identified, and no evolutionary event has been described.

For contrast:"... cryptophytes have evolved a structural switch controlled by an amino acid insertion to modulate excitonic interactions and therefore the mechanisms used for light harvesting." http://www.pnas.o...abstract

RNA-mediated events link amino acid substitutions from nutrient-dependent ecological variation to pheromone-controlled ecological adaptations in species from microbes to man via conserved molecular mechanisms. The link from biophysical constraints on plant life to animal life via nutrients is known to serious scientists and does not involve the pseudoscience of mutations and natural selection.

Nope. Mouras just wanted me to focus on your paper rather than external discussion.

nutrient-dependent

Still a useless descriptor. I don't call my car gasoline-dependent every time I talk about it. It's implicit.

Q: How did plants evolve?A: The genes and mechanism have not been identified

Your most blatant lie yet. You took a quote from my paper (out of context, I might add, when you delete the middle section between "evolved" and "through a currently unknown mechanism". I was referring to photoperiod adjustment, not evolution in general. I also specifically said the genes their effects HAVE been identified.

cryptophytes have evolved a structural switch controlled by an amino acid insertion

The insertion (a mutation) altered the function of the protein. How exactly does that refute evolution?

My research interests are in the field of evolutionary genetics, especially understanding processes occurring through or influenced by genome-level mechanisms. Active research projects in the lab use flies in the genus Drosophila for empirical studies combining molecular, cytological, and genetic approaches. Three primary research areas are currently being pursued in the lab: 1) identifying the role of chromosomal rearrangements in facilitating adaptive evolution, 2) determining the consequences of sex-linked transmission, and 3) defining common pathways of sex-chromosome evolution.

Will someone comment on the role of amino acid substitutions and retrotransposons that link ecological variation and nutrient-uptake to the metabolism of nutrients and species-specific pheromones that control the physiology of reproduction and ecological adaptations in species from microbes to man?

The anonymous fool is citing experts who can't think in terms of 'RNA-mediated events' or 'indirect genetic events' or 'genome dynamics events' or anything else that doesn't portray their ignorance of biologically-based cause and effect. They've been taught to believe in pseudoscientific nonsense about mutations and natural selection and other believers continue to cite them while ignoring anything that does not echo ridiculous theories.

Large Numbers of Novel miRNAs Originate from DNA Transposons and Are Coincident with a Large Species Radiation in Bats http://mbe.oxford...abstract

As usual, Kohl dismissed my 11 examples of experimental support without being able to point out flaws in their assumptions, methodology, or interpretation of their data, merely stating they were taught pseudoscience.

Did the bats eat, or simply mutate & radiate?

Do you know what a false dichotomy is? Where did you get the ridiculous idea that evolution supporters don't think organisms need to eat? Also, why are you under the impression eating is at odds with mutation and natural selection?

See also: http://jonlieffmd...volution"It now appears that alternative splicing is, perhaps, the most critical evolutionary factor determining the differences between human beings and other creatures."

"Widespread occurrence of phage sequences in almost all studied M. abscessus complex isolates suggests that the rate of prophage invasion is faster than the rate of mutation, implying rapid evolution of M. abscessus." http://www.biolog...abstract

The information on chromosomal rearrangements in gibbons and everything known about species diversification in microbes attests to the likelihood that biodiversity is nutrient-dependent and pheromone-controlled via RNA-mediated events that are consistently reported as if they were evolutionary events.

No evolutionary events have been described in the context of biologically-based cause and effect. Which will be more important to scientific progress:

1) The pseudoscientific nonsense about mutations, natural selection and the evolution of biodiversity?

Will someone comment on the role of amino acid substitutions and retrotransposons that link ecological variation and nutrient-uptake to the metabolism of nutrients and species-specific pheromones that control the physiology of reproduction and ecological adaptations in species from microbes to man?

Well, I'll comment if that is what you want Cher. I don't think those stinky love potions are going to increase your uptake in your finances. Matter the fact, it will probably get you landed in jail when the police hear about it.

"Much of his group's current work involves extending discoveries about translation in E. coli to the process in eukaryotes, with an eye toward human health and disease."http://www.the-sc...ualizer/

This sums up the frustration that serious scientists share when others tout their pseudoscientific nonsense about mutations, natural selection and the evolution of biodiversity, which is obviously nutrient-dependent and pheromone-controlled.

RNA-mediated events link ecological variation to nutrient-dependent amino acid substitutions that differentiate cell types. Cell type differentiation in species is controlled by the metabolism of nutrients to species-specific pheromones. The pheromones control the species-specific physiology of reproduction, which leads to ecological adaptations.

Those with no understanding of biologically-based cause and effect comment on mutations and stinky love potions.

Will someone comment on the role of amino acid substitutions and retrotransposons...

...was an invitation for someone intelligent to comment, not an invitation to an anonymous fool to comment on something he knows nothing about.

"Pseudogene-derived transcripts can regulate gene expression by generating small RNAs, regulating mRNA stability via direct binding or sequestration of trans-acting RNA decay proteins, sponging of endogenous miRNAs and promoter recruitment of epigenetic remodeling complexes. The extent to which pseudogenes are important in gene regulation and the pathogenesis of disease has so far been underappreciated for a number of reasons." http://dx.doi.org...s.13.172

The primary reason the importance of pre-mRNAs and alternative splicings have been under appreciated in the context of health and pathology is idiots who comment in discussions that might otherwise inform others who are not idiots.

Please sign in to add a comment.
Registration is free, and takes less than a minute.
Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.